Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

V1T : Summary

Code

V1T

One-letter code

X

Molecule name

1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide
OpenEye OEToolkits 1.7.6 1,3-dimethyl-2-oxidanylidene-benzimidazole-5-carboxamide

Formula

C10 H11 N3 O2

Formal charge

0

Molecular weight

205.213 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(c1ccc2c(c1)N(C(=O)N2C)C)N
SMILES CACTVS 3.385 CN1C(=O)N(C)c2cc(ccc12)C(N)=O
SMILES OpenEye OEToolkits 1.7.6 CN1c2ccc(cc2N(C1=O)C)C(=O)N
Canonical SMILES CACTVS 3.385 CN1C(=O)N(C)c2cc(ccc12)C(N)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 CN1c2ccc(cc2N(C1=O)C)C(=O)N

IUPAC InChI

InChI=1S/C10H11N3O2/c1-12-7-4-3-6(9(11)14)5-8(7)13(2)10(12)15/h3-5H,1-2H3,(H2,11,14)

IUPAC InChI key

BRBLVCVSNVSPMT-UHFFFAOYSA-N
V1T

wwPDB Information

Atom count

26 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-08-30

Last modified at

2014-09-12

Status

Released

Obsoleted

Not Assigned



V1T : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N N N 0 -2.941 2.155 -0.002
2 N05 N N05 N N N 0 -2.133 0.932 -0.003
3 C06 C C06 N Y N 0 -0.746 0.877 -0.002
4 C07 C C07 N Y N 0 0.244 1.852 0.0
5 C09 C C09 N Y N 0 1.572 1.487 0.001
6 C11 C C11 N Y N 0 1.928 0.134 0.001
7 C12 C C12 N Y N 0 0.936 -0.848 -0.001
8 C14 C C14 N Y N 0 -0.396 -0.478 -0.002
9 N15 N N15 N N N 0 -1.587 -1.2 -0.003
10 C16 C C16 N N N 0 -1.706 -2.661 -0.003
11 C20 C C20 N N N 0 -2.611 -0.326 0.002
12 O21 O O21 N N N 0 -3.79 -0.627 0.007
13 C22 C C22 N N N 0 3.352 -0.254 0.001
14 N23 N N23 N N N 0 4.31 0.695 0.002
15 O26 O O26 N N N 0 3.662 -1.43 0.0
16 H09 H H09 N N N 0 2.339 2.246 0.002
17 H011 H H011 N N N 0 -3.14 2.459 -1.03
18 H012 H H012 N N N 0 -3.884 1.967 0.511
19 H013 H H013 N N N 0 -2.399 2.948 0.512
20 H07 H H07 N N N 0 -0.028 2.897 0.0
21 H12 H H12 N N N 0 1.209 -1.893 -0.001
22 H161 H H161 N N N 0 -1.736 -3.023 1.025
23 H162 H H162 N N N 0 -2.622 -2.951 -0.517
24 H163 H H163 N N N 0 -0.848 -3.095 -0.516
25 H231 H H231 N N N 0 4.063 1.633 0.002
26 H232 H H232 N N N 0 5.245 0.44 0.002



V1T : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 N05 C N sing 1.47 N N
2 N05 C06 N C sing 1.39 N N
3 N05 C20 N C sing 1.35 N N
4 C06 C07 C C sing 1.39 N Y
5 C06 C14 C C doub 1.4 N Y
6 C07 C09 C C doub 1.38 N Y
7 C09 C11 C C sing 1.4 N Y
8 C11 C12 C C doub 1.4 N Y
9 C11 C22 C C sing 1.48 N N
10 C12 C14 C C sing 1.38 N Y
11 C14 N15 C N sing 1.39 N N
12 N15 C16 N C sing 1.47 N N
13 N15 C20 N C sing 1.35 N N
14 C20 O21 C O doub 1.22 N N
15 C22 N23 C N sing 1.35 N N
16 C22 O26 C O doub 1.22 N N
17 C01 H011 C H sing 1.09 N N
18 C01 H012 C H sing 1.09 N N
19 C01 H013 C H sing 1.09 N N
20 C07 H07 C H sing 1.08 N N
21 C09 H09 C H sing 1.08 N N
22 C12 H12 C H sing 1.08 N N
23 C16 H161 C H sing 1.09 N N
24 C16 H162 C H sing 1.09 N N
25 C16 H163 C H sing 1.09 N N
26 N23 H231 N H sing 0.97 N N
27 N23 H232 N H sing 0.97 N N



V1T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
V1T 4uyd Open in New Window Bound ligand 1 1